miRNA display CGI

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ID	Location	Perfect MFE.*	RefSeq Acc.	strand	Start Position	R_P_ratio#	P value
	Predicted miRNA align pattern
28158	3'	-53	NC_005887.1	+	18034	0.66	0.747044
	Target:  5'- -aCGCGCGCCGGAcu---GACGGccgacgauUGGg -3' miRNA:   3'- caGCGCGUGGUCUaacauCUGCC--------ACC- -5'
28158	3'	-53	NC_005887.1	+	16207	0.68	0.680975
	Target:  5'- --gGCGCGCCGGugGUUGgcGG-GGUGGu -3' miRNA:   3'- cagCGCGUGGUC--UAACauCUgCCACC- -5'
28158	3'	-53	NC_005887.1	+	28543	0.68	0.635774
	Target:  5'- -aCGCGCGCCGGGcugcugaauUUGUAGGCGu--- -3' miRNA:   3'- caGCGCGUGGUCU---------AACAUCUGCcacc -5'
28158	3'	-53	NC_005887.1	+	26176	0.71	0.460346
	Target:  5'- uGUCGCGCGCgaugaucgggUAGAUgaaaacggGgcGGCGGUGGc -3' miRNA:   3'- -CAGCGCGUG----------GUCUAa-------CauCUGCCACC- -5'
28158	3'	-53	NC_005887.1	+	40740	0.76	0.248336
	Target:  5'- -gCGCGCGCCAGGUgcaGGAUGGUGcGg -3' miRNA:   3'- caGCGCGUGGUCUAacaUCUGCCAC-C- -5'
28158	3'	-53	NC_005887.1	+	12145	0.8	0.146958
	Target:  5'- cGUCGCGCGCCAGAUUGguGACGaucgcgugacGUGGc -3' miRNA:   3'- -CAGCGCGUGGUCUAACauCUGC----------CACC- -5'
28158	3'	-53	NC_005887.1	+	25933	0.97	0.009874
	Target:  5'- cGUCGCGCACCAGAUU-UAGACGGUGGc -3' miRNA:   3'- -CAGCGCGUGGUCUAAcAUCUGCCACC- -5'

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Note:
      When operating RNAhybrid, the pipeline first calculates the perfect minimum free energy (Perfect mfe *) of a putative miRNA when the entire putative miRNA binds to a perfectly complementary target site, then it calculates the minimum free energy of RNA duplex (mfe of the miRNA/mRNA duplex), abbreviated as Rd_mfe. An alignment for which the Rd_mfe to its correspondent Perfect mfe ratio (R_P_ratio #) is more than 66% is regarded as a positive alignment as described by Krek et al. (21). The P_value is calculated by RNAhybrid.

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